March 5, 2024

“Community Genetic Editing” – Using CRISPR To Modify Genes in Multiple Cell Types Simultaneously

2 new methods allow CRISPR editing of genes in multiple cell types concurrently.
To date, CRISPR enzymes have been utilized to modify the genomes of one kind of cell at a time: They cut, erase or add genes to a specific sort of cell within a tissue or organ, for example, or to one kind of microbe growing in a test tube.

To effectively edit genes within several members of a microbial community, UC Berkeley scientists had to develop two new techniques: Environmental Transformation Sequencing (ET-Seq), leading, which permitted them to assess the editability of specific microbes; and DNA-editing all-in-one RNA-guided CRISPR-Cas transposase (DART), which enabled highly particular targeted DNA insertion into a location in the genome defined by a guide RNA. He compares this to taking a population census: It supplies unparalleled info about which microorganisms are present in which percentages, and which operates those microbes could perform within the community. The team first established a method to determine which microbes in a neighborhood are actually susceptible to gene modifying. By sequencing the neighborhood DNA before and after introducing the transposon, they were able to determine which species of microorganisms was able to include the transposon gene. They can then manipulate neighborhood genes within this closed system and track the impact on their bar-coded microorganisms.

Now, the University of California, Berkeley, group that invented the CRISPR-Cas9 genome editing technology nearly 10 years ago has found a way to add or customize genes within a neighborhood of various types all at once, unlocking to what could be called “neighborhood modifying.”
While this technology is still specifically applied in lab settings, it could be used both to modify and to track edited microbes within a natural community, such as in the gut or on the roots of a plant where hundreds or thousands of various microbes gather. Such tracking becomes essential as scientists talk about genetically changing microbial populations: placing genes into microorganisms in the gut to fix digestion issues, for instance, or changing the microbial environment of crops to make them more resistant to insects.
Without a way to track the gene insertions– utilizing a barcode, in this case– such inserted genes could end up anywhere, given that microorganisms routinely share genes amongst themselves.
To successfully edit genes within numerous members of a microbial neighborhood, UC Berkeley scientists needed to develop two brand-new techniques: Environmental Transformation Sequencing (ET-Seq), top, which enabled them to examine the editability of specific microbes; and DNA-editing all-in-one RNA-guided CRISPR-Cas transposase (DART), which enabled highly specific targeted DNA insertion into an area in the genome specified by a guide RNA. The DART system is barcoded and compatible with ET-Seq so that, when used together, scientists can place, track and assess insertion effectiveness and uniqueness. Credit: Jill Banfield laboratory, UC Berkeley
” Changing and breaking DNA within separated bacteria has been important to understanding what that DNA does,” stated UC Berkeley postdoctoral fellow Benjamin Rubin. “This work helps bring that basic technique to microbial communities, which are far more representative of how these microorganisms function and live in nature.”
While the capability to “shotgun” edit many types of cells or microbes at the same time might be beneficial in current industry-scale systems– bioreactors for culturing cells wholesale, for example, the more instant application may be as a tool in comprehending the structure of complex neighborhoods of bacteria, archaea and fungis, and gene circulation within these varied populations.
” Eventually, we might be able to remove genes that cause illness in your gut germs or make plants more effective by engineering their microbial partners,” said postdoctoral fellow Brady Cress. “But likely, prior to we do that, this method will give us a much better understanding of how microorganisms function within a community.”
Rubin and Cress– both in the laboratory of CRISPR-Cas9 creator Jennifer Doudna– and Spencer Diamond, a project scientist in the Innovative Genomics Institute (IGI), are co-first authors of a paper explaining the technique that appeared today (Dec. 6) in the journal Nature Microbiology.
From censusing to editing
Diamond operates in the laboratory of Jill Banfield, a geomicrobiologist who originated the field of community sequencing, or metagenomics: shotgun sequencing all the DNA in a complex community of microbes and assembling this DNA into the full genomes of all these organisms, a few of which likely have actually never been seen prior to and a lot of which are difficult to grow in a lab dish.
Metagenomic sequencing has actually advanced tremendously in the previous 15 years. In 2019, Diamond put together 10,000 specific genomes of almost 800 microbial species from soil samples gathered from a grassland meadow in Northern California.
He compares this to taking a population census: It supplies unrivaled information about which microbes are present in which proportions, and which functions those microorganisms could carry out within the community. And it allows you to infer complex interactions among the organisms and how they may interact to achieve important community advantages, such as fixing nitrogen. These observations are only hypotheses; new techniques are needed to actually test these functions and interactions at a community level, Diamond stated.
” Theres this idea of metabolic handoffs– that no specific microorganism is carrying out a huge string of metabolic functions, however for the a lot of part, each individual organism is doing a single action of a process, and that there needs to be some hand-off of metabolites between organisms,” he said. “This is the hypothesis, however how do we in fact prove this? How do we get to a point where were no longer simply enjoying the birds, we really can make a couple of controls and see whats going on? This was the genesis of neighborhood modifying.”
The research study team was led by Banfield, UC Berkeley teacher of earth and planetary science and of ecological science, policy and management, and Jennifer Doudna, UC Berkeley professor of molecular and cell biology and of chemistry, Howard Hughes Medical Institute investigator and co-winner of the 2020 Nobel Prize in Chemistry for the invention CRISPR-Cas9 genome modifying.
The group initially developed an approach to identify which microbes in a neighborhood are really susceptible to gene modifying. By sequencing the neighborhood DNA before and after introducing the transposon, they were able to determine which types of microbes was able to incorporate the transposon gene.
Cress then established a targeted shipment system called DNA-editing All-in-one RNA-guided CRISPR Cas Transposase (DART) that utilizes a CRISPR-Cas enzyme similar to CRISPR-Cas9 to home in on a particular DNA series and place a bar-coded transposon.
To evaluate the DART technique with a more sensible microbial community, the researchers took a stool sample from a baby and cultured it to produce a steady community made up mainly of 14 various types of microorganisms. They had the ability to edit specific E. coli stress within that community, targeting genes that have been associated with illness.
They can then manipulate community genes within this closed system and track the result on their bar-coded microbes. These experiments are one element of a 10-year program moneyed by the Department of Energy called m-CAFEs, for Microbial Community Analysis and Functional Evaluation in Soils, which seeks to comprehend the action of a simple yard microbiome to external modifications.
Referral: “Species- and site-specific genome editing in intricate bacterial neighborhoods” by Benjamin E. Rubin, Spencer Diamond, Brady F. Cress, Alexander Crits-Christoph, Yue Clare Lou, Adair L. Borges, Haridha Shivram, Christine He, Michael Xu, Zeyi Zhou, Sara J. Smith, Rachel Rovinsky, Dylan C. J. Smock, Kimberly Tang, Trenton K. Owens, Netravathi Krishnappa, Rohan Sachdeva, Rodolphe Barrangou, Adam M. Deutschbauer, Jillian F. Banfield and Jennifer A. Doudna, 6 December 2021, Nature Microbiology.DOI: 10.1038/ s41564-021-01014-7.
The research study was supported by m-CAFEs (DE-AC02-05CH11231) and the National Institute of General Medical Sciences of the National Institutes of Health (F32GM134694, F32GM131654).
Other co-authors of the paper are Alexander Crits-Christoph, Yue Clare Lou, Adair Borges, Haridha Shivram, Christine He, Michael Xu, Zeyi Zhou, Sara Smith, Rachel Rovinsky, Dylan Smock, Kimberly Tang, Netravathi Krishnappa and Rohan Sachdeva of UC Berkeley; Trenton Owens of Berkeley Lab; and Rodolphe Barrangou of North Carolina State University.